4UZS

Crystal structure of Bifidobacterium bifidum beta-galactosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpah-Galactose.

Godoy, A.S.Camilo, C.M.Kadowaki, M.A.Muniz, H.D.S.Santo, M.E.Murakami, M.T.Nascimento, A.S.Polikarpov, I.

(2016) FEBS J. 283: 4097

  • DOI: 10.1111/febs.13908
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tra ...

    In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme kcat without significant modification in its Km , whereas mutations Tyr289Phe and His371Phe simultaneously decreased kcat and increased Km values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable.


    Organizational Affiliation

    Departamento de Física em São Carlos, Universidade de São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-GALACTOSIDASE
A, B, C
689Bifidobacterium bifidum (strain S17)Mutation(s): 0 
Gene Names: lacZ2
EC: 3.2.1.23
Find proteins for E3EPA1 (Bifidobacterium bifidum (strain S17))
Go to UniProtKB:  E3EPA1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POL
Query on POL

Download SDF File 
Download CCD File 
A, B, C
N-PROPANOL
1-PROPONOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.701α = 90.00
b = 99.241β = 106.47
c = 110.757γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 1.2: 2016-12-07
    Type: Database references
  • Version 1.3: 2017-07-05
    Type: Data collection